hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data11/genetics/InterProScan/iprscan/data/Pfam Sequence file: /cdna4/rodent/full/goal/mbg/mbg00277/w3open/interpro/cnk_1/seq.in - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: mKIAA0940 ( 722 res) mbg00277 Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, o 36.1 7.8e-07 2 Extensin_2 Extensin-like region -127.5 0.16 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Extensin_2 1/1 33 361 .. 1 385 [] -127.5 0.16 RRM_1 1/2 467 540 .. 1 74 [] 27.2 0.00021 RRM_1 2/2 575 646 .. 1 74 [] 8.9 0.023 Alignments of top-scoring domains: Extensin_2: domain 1 of 1, from 33 to 361: score -127.5, E = 0.16 *->lltlvvalvslslpseasakYsYsSPPPpekpYvYkSPPpPspkyvy +l + + + + ps + sS P P s + mKIAA0940 33 QQQLQPEPGAAEAPSTPL-----SSEIPK---------PEDSSAVPA 65 kSPPPpkkpYvYsSPPPPsyvykSPPPPkpyvYkSPPpPkyvYkSPPpPv SP + PP P P + +SP P + PP mKIAA0940 66 LSPASA----------PP-----APNGPDKMQMESPLLPGLSFHQPP--- 97 ykYkSPPPPthsppPpyvykSPPPPpk......kyvykSpPp.ptPv... + PPPP p p SP + +++++ v S ++tPv+++ mKIAA0940 98 ---QQPPPPQ-EPTAPGASLSPSFGSTwstgttNAVEDSFFQgITPVngt 143 YkYkSPPPPp.yvYkspPpPvkk.ripyvYkSPPPPpPYvYkSpPppvkk ++ P +++v+ P + + PPPP P pP p mKIAA0940 144 MLFQNFPHHVnPVFGGTFSPQIGlAQTQHHQQPPPPAP----QPPQPA-- 187 yiyksppppephkYvYkSPPPPpPYvyesvpeqkikYvYkSPPPPkksYk pp +p + +SP P+ + + q+ Y P + mKIAA0940 188 ----QPPQAQP-SQQRRSPASPS----QAPYAQRSAAAYGHQPIMTS--- 225 spsppkyVYkSpPpPvipykYkSPPPPkkkyspaPrkpyvYkSPPPPtyv ps + V + + + + + + ++ P P mKIAA0940 226 KPSSSSAVAAAAAAAA---ASS----ASSSWNTHQSVNAAWSAPSNPWGG 268 YkSpPpPyk..pptppkiyksPPPPtPvyvYkspPpippiksssppPvyv + P++ ++ P P P+ k p s P+ mKIAA0940 269 LQAGRDPRRavGVGVGVGVGVPSPLNPISPLKKPFS-----SNVIAPPKF 313 YkSpPppvysPPPPyvYssPPPPvyvynsaPvykksPPkhhYiYsSPPPp + +P ++s ++ n P + +s P + S mKIAA0940 314 PRAAPLTSKSWMEDNAFRTDNG----NNLLPFQDRSRPYDTFNLHSLENS 359 hh<-* + mKIAA0940 360 LM 361 RRM_1: domain 1 of 2, from 467 to 540: score 27.2, E = 0.00021 *->lfVgNLppdtteedLkdlFskfGpiesikivrD.ttretgrskGfaF +fVg+Lppd++e+++ + F+ fGp ++ +++ ++++ +kG+aF mKIAA0940 467 VFVGGLPPDIDEDEITASFRRFGPL-VVDWPHKaESKSYFPPKGYAF 512 VeFedeedAekAldalnGkelggrelrv<-* F+ e+++++ +da+ + + + mKIAA0940 513 LLFQEESSVQALIDACLEEDGKLYLCVS 540 RRM_1: domain 2 of 2, from 575 to 646: score 8.9, E = 0.023 *->lfVgNLppdtteedLkdlFsk.fGpiesikivrDttretgrskGfaF +fVg+ p+ + +L + +G++ + i +D +e + +kG + mKIAA0940 575 IFVGGVPRPLRAVELAMIMDRlYGGVCYAGIDTD--PELKYPKGAGR 619 VeFedeedAekAldalnGkelggrelrv<-* V F ++ + +A++ +l + + mKIAA0940 620 VAFSNQQSYIAAIS-ARFVQLQHNDIDK 646 //